Comparative Methylomics Between Domesticated and Wild Silkworms Implies Possible Epigenetic Influences on Silkworm Domestication

Whether epigenetic changes play roles in domestication of organisms is still an open question. Recent growing field on insect methylomics indicate that epigenetic regulation in insects may have effects on diverse biological processes. Here we firstly indicated an active methylation system in the model domestic insect, silkworm. Specially by embryonic RNA interference, we reveal that knockdown of silkworm dnmt1 caused decreased hatchability. We further survey the silkworm methylome at single-base resolution using Illumina high-throughput bisulfite sequencing (MethylC-Seq) and found that CG methylation is substantially enriched in gene bodies and is positively correlated with gene expression levels, suggesting it has a positive role in gene transcription. Based on the above results, we comprehensively compare silk gland methylomes between domesticated (Bombyx mori) and wild (Bombyx mandarina) silkworms. Two -fold more differentiated mCs were in domesticated than in wild silkworms, suggesting a trend of fixation of DNA methylation during silkworm domestication. Particularly we identify a methylation differential gene with domestication signal and imply that it is more likely epigenetic than genetic changes that caused the expression changes during domestication. Another gene is also interesting in that correspondent expression changes in domesticated silkworms may be related to evolution of silk gland. Our results imply epigenetic influences during domestication, which bears long time historical controversy on acquired inheritance.